The Cheapest Genome Sequence Ever: For Real?

This story has been updated.

A biotech startup company promises to decipher the human genome for $5,000 — a price tag that could literally change the world, making high-resolution genetic scans available to relatively low-budget laboratories, and literally reshaping the questions that scientists can ask.

But is a $5,000 sequence, like a camera from a Times Square electronics store or a street-corner Rolex, just too cheap to believe? The test hasn’t yet been independently validated, but scientists say the deal appears to be real.

"I have great confidence that it’s right," said Lawrence Berkeley National Lab geneticist Michael Eisen. "I don’t know exactly what the underlying method is, but George Church isn’t a kidder."

George Church is a Harvard University geneticist who helped found the Human Genome Project and was responsible for the first commercial genome sequence. He’s also an adviser to the Mountain View, California-based Complete Genomics, provider of the $5,000 genome — and joining Church is Illumina co-founder Mark Chee, Institute for Systems Biology president Leroy Hood and Massachusetts Institute of Technology bioengineer Douglas Lauffenburger.

It’s a veritable Who’s Who of genomic expertise, and the company’s scientific director is Radoje Drmanac, a Human Genome Project group leader. It’s an extremely credible bunch who’ve offered to bring the price of genome sequencing down from it’s current $100,000 price tag and toward the long-awaited, near-mythological $1,000 genome.

And even at $5,000, the consequences would be enormous: Human genetic research, which is now focused on just a few genomic regions, and ignores types of variation that can’t easily be measured, would finally be able to assume its full form.

"It’s going to change again how we think about approaching biomedical research," said Jackson
Laboratory genome informaticist Carol Bult, who called the implications
"breathtaking."

The cost and difficulty of sequencing genomes has forced medical geneticists to take a painstaking and limited approach to their work, necessarily looking only at a few genes or mutations. Even whole genome association studies — the gold standard of modern genetics — are misleadingly named: Geneticists search for similarities and differences between people at a handful of genomic locations that are most likely to vary between people, but still ignore most of the genome. Truly-named whole genome associations don’t yet exist.

"The remaining variation represents only a small fraction of the variation in the human genome," said Eisen, "but there’s reason to suspect that there’s important things contained in that variation."

Those variations, known as Single Nucleotide
Polymorphisms, or SNPs, are but one type of genomic difference. There are also copy number variations and errors of insertion and deletion —
the rough equivalent of having entire sentences, even pages, torn out or shoved into the "blueprint of life."

"There’s a whole world of genetic variation that SNPs don’t capture," said Eisen. "You’re always going to have an incomplete view of the genome if you only have
SNPs."

As researchers are able to measure non-SNP variations, they can connect them to health and development outcomes in the way that basic genetic mutations are now associated with disease or personal characteristics. This wouldn’t give scientists a full picture of human health and development — far from it — but it’s a key part of the foundation.

Once a more nuanced view of the genome is realized by researchers, it’ll make its way to consumers.

"We’re certain that research communities will adopt this, when it gets to an affordable cost," said Linda Avey, co-founder of personalized genomics company 23andMe. "We’re energized that they’re making the progress they are."

Bult and Eisen agreed that Complete Genomics’ $5,000 genome is just a preview of what’s coming.

"There’s a real explosion coming in cheap genome sequencing technologies," said
Bult. "This is probably just the first one to press."